I doubt the troopers there could have gunned down Anakin, anymore that the remaining clone troopers in the Jedi Temple were able to gun down Obi-Wan or Yoda.

There's a big difference between this hypothetical situation and the Obi-Wan and Yoda situation: Yoda and Obi-Wan were ready for the clones with their lightsabers drawn, and they obviously started at α normal distance. In this instance, Vader was standing less than a yard away from the clones and didn't even have his lightsaber on. It would be as easy for the clones to kill him then as it would be any of the Jedi in Order 66 (as seen in the movie).

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Theoretically, it's likely that they were conditioned to accept the Sith way of Apprentice overcoming the Master, and then rather than kill the "traitor", follow him instead.They followed a Sith Lord like Palpy without question, after all.

That's insane. Why would Palpatine make it easier for someone to kill him and get away with it? Palpatine specifically crafted the Empire's government and military (especially the stormtroopers) to be loyal to him alone. Ultimately, everyone answered to him, and the clones had no reason whatsoever to accept the execution of their leader over some arbitrary rule in an obscure culture that they didn't even know about.

"There is something going on in time and space, and beyond time and space, which, whether we like it or not, spells duty." -Winston Churchill

"For of all sad words of tongue or pen, The saddest are these: 'It might have been!'" -John Whittier